Thanks Peter

I managed, on the second attempt, to get past the gnu coreutils problem. Zipho noticed a weird lockup though: conftest that seemed to be from the gnu coreutils install wanted to listen on port 4001, which is the same port our uwsgi server listens on. The install has now completed but I'll try and find time to go back and verify this.

On the second attempt perl seems to be installing, so I'll see if it completes or hits the error you're mentioning.

Peter

On 22 February 2016 at 11:34, Peter Briggs <peter.briggs@manchester.ac.uk> wrote:

Hi Peter

I think that package_perl_5_18 in the tool shed is broken, I came across the same error last week on both our production instance and a local 'test' instance (both v15.10).

My suspicion is that the following lines are to blame:

...
                <action sha256sum="5c69adb47ab828aa3e8b5be89b88cd49c6a0d0dae2e8b3bca17a9ce699190e7b" type="download_file">
http://www.cpan.org/authors/id/A/AP/APEIRON/local-lib-1.008009.tar.gz
                </action>
                <action type="shell_command">tar xfvz local-lib-1.008009.tar.gz</action>
...

Looking at the Galaxy internals I believe that the 'download_file' action automatically unpacks the archive and cd's into the resulting directory, hence the failure for the subsequent 'tar xfvz ...' command. But I haven't had the time yet to verify this or create a patch to see if the removal of this line addresses the problem.

I don't think I've seen the problem with 'package_gnu_coreutils_8_22' that you describe however so it may be that my hypothesis is not correct.

HTH

Best wishes

Peter

On 22/02/16 05:10, Peter van Heusden wrote:

Hi there Eric and others

I tried to install the JBrowse tool on a dev branch server running on an
Ubuntu 14.04 VM.

It got stuck at the package_gnu_coreutils_8_22 dependency (revision
ac64dfe4b1fb) - this ended up in "Installing tool dependencies" state.

If I go look at the tool details it highlights errors
in package_perl_5_18 which in turn refers to errors in gnu_coreutils
(just "Error" state) and then this more informative failure for perl:

"tar (child): local-lib-1.008009.tar.gz: Cannot open: No such file or
directory
tar (child): Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error is not recoverable: exiting now"

I wonder if this is a sign of a download error?

Digging a bit more I find the error "Shutting down process id 21094
because it generated no output for the defined timeout period of 3600.0
seconds." for gnu_coreutils.

I'm trying to do a reinstall of the gnu_coreutils and perl packages to
see if I can get further.

Peter

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--
Peter Briggs peter.briggs@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482